Catalog

Catalogs or Collections are administrative lists with inconsistent relationships to
physical items. Therefore, a Cataloged Item is an abstraction, i.e.,
it is an item that has been cataloged, and hence defined, by the
administrator of a catalog.

The term “specimen” is used synonymously with “cataloged item” throughout Arctos.

Catalog Number

Cataloged_Item . Cat_Num VARCHAR2(40) not null

Catalog Number is the identifier assigned to a
Cataloged Item. It must be unique (case-insensitive) within a particular
catalog. Arctos currently supports three formats of catalog number.

Integer: Catalog numbers must be positive integers. Arctos
provides tools to predict the next number (e.g., data entry can
leave catalog number blank), find gaps in sequences, search by
ranges, clone full records, and provide GUIDs of the “expected” format. Sort may be numeric (1,2,,3…20). Only this format
comes with these tools and abilities, and it is often worthwhile to
convert existing mixed-string catalog “series” to Integer catalog
numbers and store the old numbers as other IDs.

Prefix-Integer-Suffix: An integer is required, and may be
accompanied by a prefix and/or suffix. The concatenation of
prefix-integer-suffix must be unique. No predictive tools
are available. Search is by the concatenation or substrings thereof. Sort will be character (1,2,…20…3).

String: Any unique non-NULL string is accepted. No predictive
tools are available. Search is by the string or
substrings thereof. Sort will be character (1,2,…20…3). Characters “/” (forward slash) and “ “ (space) are currently prohibited.

Cataloged Item Type

Cataloged_Item . Cataloged_Item_Type VARCHAR2(20) not null

A code table is available to explicitly label various types of cataloged material.

Remarks

Coll_Object_Remark . Coll_Object_Remarks VARCHAR2(4000) null

Use remarks to document non-standard information pertaining to the specimen.
Do not use remarks for any information which could be recorded with more structure elsewhere, including
remarks better stored with a part, event, or any other “piece of the specimen.”

Entered By

Coll_Object . Entered_Person_ID NUMBER(22) not null

Agent creating the catalog record in Arctos.

Entered Date

Coll_Object . Coll_Object_Entered_Date NUMBER(7) not null

Date on which the record was created.

Edited By

Coll_Object . Last_Edited_Person_ID NUMBER(22) null

Agent last editing the catalog record.

Edited Date

Coll_Object . Last_Edit_Date NUMBER(7) null

Date on which the record was last edited.

Flags

Coll_Object . Flags VARCHAR2(20) null

Flags mark a specimen as missing information during the entry process. It is sometimes more convenient to bulkload data after the
specimen record exists than to enter data with the specimen; flags serves as a marker to facilitate easily locating those specimens.

Associated Species

Coll_Object_Remark . Associated_Species VARCHAR2(4000) null

Free-text description of species associated with the specimen.

Guid Prefix

Collection . GUID_Prefix VARCHAR2(20) not null

Catalogs are most usefully defined by way of a GUID Prefix,
which in conjunction with catalog number forms a unique identifier
within Arctos, and in conjunction with Arctos’ URI forms a Globally
Unique Identifier (GUID) for the specimen record. GUIDs, once formed,
must never be allowed to change or expire. See deleting specimens
for guidelines. All specimen citations should occur by way of GUID. Note that while GUID Prefix
generally appears to be a concatenation of institution and collection code, it is in fact an independent
concept; several collections from an institution may use the ‘Herb’ collection_cde
(e.g. for vascular plants, cryptogams, and marine algae collections, for example).

Collection

Collection . Collection VARCHAR2(50) not null

A short name for a particular collection type. For
example:

Mammal Specimens

Collection Code

Collection . Collection_Cde VARCHAR2(5) not null

Collection Code links catalogs to collection-type-specific code tables. Values are generally descriptive (“Mamm” or “Bird”), but
no deeper meaning exists.
Existing collection_cde values are in a code table.
Exploring the “filter” option of Attribute Type
will provide an idea of how a collection type has been used.

Description

Collection . Descr VARCHAR2(4000) null

An extended name/description of the collection. For example:

University of Alaska Museum, Mammal Collection

Parasite Collection at the Museum of Southwestern Biology,
Albuquerque, NM

Kenelm W. Philip lepidoptera collection

Institution Acronym

Collection . Institution_Acronym VARCHAR2(20) null

Abbreviation of the institution that hosts the
catalog. For example, “MVZ” for Museum of Vertebrate Zoology, “UAM” for
University of Alaska Museum (of the North), “MSB” for Museum of
Southwestern Biology. Generally, these values are the same as those
traditionally used for specimen citations within discipline-specific
publications. There is now a demand for globally unique specimen
identifiers on the Internet, and at least one registry for such abbreviations has been
established.

Searching

From SpecimenSearch, Catalog Number accepts arguments of several forms.
The following table is illustrative.

Input

Matches

Why

12

12

No-operator inputs are string matched.

12-14

12, 13, or 14

Dash-separated smaller–>larger integers specify a range. Note that there is a 1000-item limit on ranges and lists.

=12-14

12-14

”=” (equals) prefix overrides all other operators and assumptions; only a matching string is returned.

12-11

12-11

“Second” item is smaller than “first” item; not considered as range.

12-0110

12-0110

“Second” item is zero-padded so not considered an integer; not considered as range.

12,13,14

12, 13, or 14

Commas are treated as list delimiters unless the value is prefixed with an equals sign. Note that there is a 1000-item limit on ranges and lists.

12,13a,14

12, 13a, or 14

Commas are treated as list delimiters unless the value is prefixed with an equals sign. Neither catalog numbers nor list elements must be numeric. Note that there is a 1000-item limit on ranges and lists.

%12%

12, 121, 12a, 999483612345, ….

”%” is “match anything.” This matches anything CONTAINING 12.

%12

12, 112, AABC-5-a12, ….

”%” is “match anything.” This matches anything ENDING WITH 12.

_12

012, a12, 912, ….

“_” is “match any single character.”

1_2

102, 112, 1A2, ….

“_” is “match any single character.”

Locating Specimens by Identifier

Each specimen in Arctos receives (and is define by) a single catalog number, along with any
number of identifying numbers, often referred to as “Other IDs.” There
are several ways, each with their own limitations, to search these
numbers. The data available for searching vary wildly based on what
collectors have recorded and what collections have entered. Some
exploration is often involved in finding a particular set of specimens.

Other IDs

Other Identifiers, like catalog numbers, have three components: A
prefix, an integer, and a suffix. Individual collections define how
these components should be used, acceptable values, and how data are to
be entered, and these decisions affect what sorts of queries are
possible. It is often not possible to deduce these rules and practices –
contact us if you need
help.

To get Other ID search, click More Options on the Identifiers pane of
SpecimenSearch.

This will provide options to select Other ID Type and to provide an
Other ID Number. (We generally use “number” in the sense of a license
plate rather than an integer.) Additionally, you can choose whether the
number is an exact match or a “contains” match. Exact match searches are
case-sensitive.

It’s often unclear what type of ID might have been assigned to a number,
and the descriptions currently do little to clarify that problem. It is
therefore possible (and often most practical) to search by the number
component, entirely ignoring ID Type.

The above example finds all specimens with any type of identifier
(except catalog number)

containing the string 123. As of this writing, that search returns
9330 specimens. Additional criteria, coupled with Arctos’ sorting
capability, is hopefully enough to find the specimen data of interest.

To get all search options, click Customize (near “Show More Options”),
select a “My Other Identifier” (which will also then appear in results
and on various forms), and choose “Show 3-part ID Search.”

Click Close and the form will reload with total of eight search options.
For this example, we’ll use Collector
Number.
The simplest use case is to search for a string, here 1234:

This sends the query upper(customIdentifier.Display_Value) LIKE
‘%1234%’ (display_value is a concatenation of prefix, number, and
suffix). This returns specimens with Collector Numbers of:

ABC-1234-X

1234

1234567

regardless of how the data were entered and are stored. (“ABC-1234-X”
could be entered as prefix=”ABC-1234-X” or as prefix=”ABC-“,
number=”1234″, suffix=”-X”; “1234” could have been entered as a number
or as a prefix.)

Changing the dropdown from “contains” to “is” will, of the above
examples, return only “1234.”

The “in list” option accepts a comma-separated list of values.

The above example sends SQL upper(customIdentifier.DISPLAY_VALUE) IN
(‘A’,’B’,’C’), and as of this writing returns three specimens:

The in range option works only for enforced-integer types of identifiers
(currently only AF and NK). Attempting to use it for collector number
will result in a datatype mismatch and return an error.

Three-part search to the rescue! (At
least in the cases where data are entered correctly.) All of the above
deal with the concatenation of prefix, number, and suffix. It is also
possible to search these independently. Search for integer
component=1234:

to send SQL customIdentifier.other_id_number = 1234.

This is a numeric match of the numeric part of other IDs. It will not
find specimens which have the numeric information entered into prefix.
This information is not available to public users, but is evident from
the edit form. This specimen will NOT be found with the previous search!

Prefix and suffix work similarly. This search:

sends SQL AND upper(customIdentifier.other_id_prefix) LIKE ‘%A%’ AND
customIdentifier.other_id_number = 123 (note prefix is a CONTAINS
match and is not case-sensitive) and returns these specimens:

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Understanding Cataloged Items

We address assigning catalog numbers to material with a few brief
examples.

In short, we strongly recommend cataloging the item of scientific
interest: the material that Researcher #2 will ask to borrow for
confirmation when they find your citations in GenBank or publications.
Any other approach complicates tracking citations and data management.

We present as example a brief list of things that may be cataloged in
Arctos.

A biological individual

Standard practice in vertebrate collections, and the method we
strongly encourage when possible. Biological individuals are
generally the item of scientific interest, and the thing a
future researcher will wish to examine if attempting to
replicate results.

A biological individual and their parasites

Common practice in vertebrate collections, but makes locating or
citing a parasite more complicated and less reliable than it
needs to be. Rather, we recommend cataloging the host,
cataloging the individual parasites (or donating them to someone
who can), and establishing proper relationships.

A lot (e.g., all intestinal parasites from an individual; all
members of a taxon from a time and place, or all insects from
a trap)

While lots are a convenient and sometimes necessary ”working
group,” (e.g., due to the number of individuals involved or
the available expertise in identification) we strongly
discourage making lots available for citation. Insect
collections often loan lots, and the borrowing researcher will
sort the lot to individuals for which they are provided catalog
numbers, a situation we find acceptable. Attaching cryptic and
fragile “individual tags” to members of a lot when someone uses
a specimen for molecular analysis makes little sense to us.

An occurrence (e.g., each instance of the capture of
an individual)

This situation inevitably leads to confusing citations and bad
science when an individual sampled multiple times at multiple
locations is assumed by users to be multiple
distinct individuals. Arctos supports cataloging encounters as
specimen events under one cataloged item.

Your “share” of an individual (e.g., tissues; the bones being
cataloged elsewhere)

Similar to occurrences in that this leads to multiple
identifiers being assigned to an individual (and potentially the
two being compared in a study), this should be avoided
when possible. When unavoidable, both systems should support
resolvable identifiers and link to each other, and specimen
downloads should include the relationship. Arctos also adds a
distinctive style to “same individual as” specimens.

Various parts of an individual (e.g., tissues cataloged separately
from vouchers)

This denormalization of data inevitable leads to divergence and
confusion (not to mention increased curatorial workload), in
addition to the aforementioned implications of assigning the
item of scientific interest multiple primary identifiers. Having
reconciled the data in similar systems, we cannot possibly be
vigorous enough in discouraging the continuation of
such methodology.

An entire collection

We include this to stress the fact that cataloged items are
wholly arbitrary concepts assigned to whatever someone wanted
to catalog. That is, the scientific value of a cataloged number
is entirely up to the person deciding upon the material
to catalog.

Several of the above

An individual or physical item (or anything else) may have any
number of catalog numbers within or across collections. While
this is occasionally necessary for various political or
administrative reasons, we strongly encourage avoidance, and the
proper use of resolvable OtherIDs (in a system which
supports them) to clearly link all of the components of the item
of scientific interest together when multiple numbers are for
some reason necessary. (see http://mailman.yale.edu/pipermail/nhcoll-l/2016-March/009178.html)

Defining Collections

Collections in Arctos are wholly administrative. Collections may be comprised of similar taxa (e.g. mammals), of
various taxa organized for some purpose (such at the Hildebrandt Collection at MVZ),
by legacy usage, or anything else. The sole functional or technical consideration is code tables, which are tied to collection type
(collection_cde). For example, contrast Attributes available to a
Mamm collection
versus a Para collection.

Legacy collections often exist for various reasons, and these may have duplicate catalog numbers, unpredictable formats which may
confuse users, or contain arbitrary divides which no longer make sense. Combining these into a unified collection in Arctos is generally
trivial, and Arctos provides various mechanisms (such as actionable identifiers and
redirects) to ensure that no functionality is lost. Collections with “less citable” catalog number schemes are
unlikely to support actionable citations, and so little is lost if the
“traditional catalog numbers” are subsumed under a “citable catalog
number.” This approach has been used to unify and disambiguate several
Arctos collections; we find tradition little excuse to go forward under
systems which discourage good science.

Deleting records from Arctos

Encumber
the record(s) to be deleted. Create an appropriate encumbrance
first, if necessary. Records may be flagged from individual
specimens, or en masse by using the Manage widget
from Specimen Results of a search. Once records are flagged, they may be deleted
by users with the appropriate privileges.

Find the encumbrance (under Tools). Click See Specimens and
carefully review what you’re about to delete.

From Manage Encumbrances, click Delete Encumbered Specimens. You’ll
again be asked to review your decision, and must click the proceed
button at the bottom of the page to delete the records from
the database.

Note that there may be reasons to keep masked records in the database
instead of deleting them.

Recataloging Specimens

It is sometimes necessary to move cataloged items from one collection or
catalog number to another. When doing so, it is important to maintain a
way of finding the specimen by its original identifiers. In this, be as
specific as possible. Use specific identifier types and GUIDs if
possible. (See more at Other IDs.)

Ensure that the “old” URL returns a 404 HTTP status code. You may do
this in two ways:

Delete the specimen. All users will then get the redirect.

Encumber the specimen with a “mask record” encumbrance. Users
who do not have rights to bypass the encumbrance (e.g., all
public users) will then be redirected, while operators will be
able to continue to access the record.

Insert into table REDIRECT (Manage Data/Tools/Redirects) old and
new paths. For example, if DGR:Mamm:123 is recataloged as
MSB:Mamm:456, enter: old_path=/guid/DGR:Mamm:123;
new_path=/guid/MSB:Mamm:456.